Egypt, gunning for an unprecedented third title in a row, had already secured top spot in the group after victories over Nigeria and Mozambique.
Nigeria, who have six points, went through with a 3-0 win over Mozambique who were sent packing along with Benin.
Egypt will play their quarter-final on Monday against the second-placed team in Group D, Cameroon, Zambia, Tunisia or Gabon.
Egypt, who stretched their unbeaten run at the African Nations Cup to 16 games, were quickly on the attack in Benguela, playing their neat passing game in front of a half-empty stadium.
They went in front after seven minutes when defender Ahmed Al Muhammadi unleashed a long range cross which caught goalkeeper Yoann Djidonou off guard.
Ahmed Raouf's header was then parried away by Djidonou, only for Emad Motaeb to latch on to the ball and make it 2-0 after 23 minutes.
In a lively game played against the monotonous drone of plastic horns, Benin posed little threat in attack.
Motaeb came close to a third shortly after resumption but he wasted his one-to-one with Djidonou.
Benin had their best chance after the hour when substitute Mohamed Aoudou's header was tipped over the bar by Essam El Hadari.
Egypt finished strongly but several Djidonou superb saves denied them a third.
